BC Centre for Disease Control Public Health Laboratory
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135 repositories
PCR_strainer
Publicpangolin-nf
PublicRun pangolin on multiple output directories from BCCDC-PHL/ncov2019-artic-nfncov2019-artic-nf
Publicncov-tools-nf
PublicA nextflow-based workflow for running ncov-toolswasteflow2
Publicriboscope
Publiccovflo
PublicNextflow pipeline for generation of BCCDC routine SARS-CoV-2 phylogenetic trees to be visualized with Auspice.routine-assembly
PublicPipeline for performing routine genome assemblyillumina-uploader
Publicnf-shovill
Publicabricate-nf
Publicmlst-nf
PublicRun mlst on multiple samples with integrated quality control.referenceseeker-nf
Publicauspice
Publicauto-fastq-symlink
PublicAutomated symlinking of sequence datahcv-nf
PublicGenomic analysis pipeline for genotyping of Hepatitis C Virusfluflo
PublicNextflow pipeline for generation of phylogenetic trees to be visualized in Auspice.nfflu-results-collector
Publicauto-cpo
PublicAutomation of Genomic Analyses for Carbapenemase-Producing Organisms (CPOs)downsample-reads
Publicsnippy-variants
PublicPerform read mapping and variant calling using snippycutadapt-nf
Publicauto-hcv
PublicAutomated genomic analysis of HCV sequence dataauto-irida-uploader
PublicAutomated uploading of sequence data into IRIDA instances, used in conjunction with auto-irida-azure-uploadtaxon-abundance
Publicalignment-variants
PublicPipeline to perform alignment & variant calling on whole-genome sequence datacgmlst-clustering
PublicScripts to support clustering of cgMLST allele profiles
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